3OY2

Crystal structure of a putative glycosyltransferase from Paramecium bursaria Chlorella virus NY2A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298100mM Tris-HCl pH7.0, 20% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.4163.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.615α = 90
b = 246.941β = 90
c = 67.17γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMarCCD 3002008-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35099.80.0740.0745615756045
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.32.3899.60.494.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.31130.195615753234284399.350.234760.2330.2678RANDOM15.933
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.62-0.17-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.37
r_dihedral_angle_3_deg22.176
r_dihedral_angle_4_deg20.212
r_dihedral_angle_1_deg6.934
r_scangle_it2.985
r_scbond_it1.971
r_angle_refined_deg1.778
r_mcangle_it1.192
r_mcbond_it0.624
r_chiral_restr0.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.37
r_dihedral_angle_3_deg22.176
r_dihedral_angle_4_deg20.212
r_dihedral_angle_1_deg6.934
r_scangle_it2.985
r_scbond_it1.971
r_angle_refined_deg1.778
r_mcangle_it1.192
r_mcbond_it0.624
r_chiral_restr0.152
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6202
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling